Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_011382728.1 AMB_RS01425 bifunctional aldolase/short-chain dehydrogenase
Query= metacyc::BSU31220-MONOMER (689 letters) >lcl|NCBI__GCF_000009985.1:WP_011382728.1 AMB_RS01425 bifunctional aldolase/short-chain dehydrogenase Length = 679 Score = 371 bits (952), Expect = e-107 Identities = 229/694 (32%), Positives = 358/694 (51%), Gaps = 35/694 (5%) Query: 2 VKHIWDSERAAQL-----PKGVEE----LVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFR 52 +K +W A P+GV VY + L+G D + GGGNTS KTT D Sbjct: 1 MKSLWSDADAESFVTRYAPEGVNRDLALRVYTTRLLGGDPRLVLHGGGNTSCKTTVTDLL 60 Query: 53 GREIEVMWVKGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHP 112 G +EV+ VKGSG D+ ++ ++L + L + D + DE+MVDY +++S P Sbjct: 61 GETVEVLCVKGSGWDMGDIEPAGLPAVRLAPLLKLRRLDSLSDEDMVDYQRGNLMNSASP 120 Query: 113 RPSIETLLHAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSK 172 PS+ETLLH FLP+K +DHTH A++S+ +G+ +A ++YG R +VPY+ PGF L+K Sbjct: 121 NPSVETLLHGFLPHKFIDHTHSTAVLSLVDQPDGEALAREVYGTRMGYVPYIMPGFALAK 180 Query: 173 MIAEGVANNPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGK 232 AE +P E +++ KHG+ T+ + + T Y+ I ++ AEQ + G Sbjct: 181 KAAEIYEQDPTVEGLILVKHGIFTFADNARTAYELMIEMVTLAEQRLEKGRKPLVAATGL 240 Query: 233 RYQPLPEDKRKQILAGIMPVIRGAVSE-EKKMILSYDDHDDVLEFVNSVQAPALSQIGAA 291 P P LA + P++RG ++ K+ IL + + + +V+ + SQ G Sbjct: 241 PKDPAP-------LAEVAPILRGLLANGPKRRILDFRTSNAIRAYVDGAEIGRYSQQGVV 293 Query: 292 CPDHLVHTKRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQQDGDQI---F 348 PDH + TK P+ + PE + A+ ++ +E+F ++Y AYF+RN Q I Sbjct: 294 TPDHTIRTKNWPVVLP-APEAGKTAEWAEAAQAAIESFEAKYHAYFSRNNQRLGNIKTEL 352 Query: 349 ESAPRVILIPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEY 408 + P V L+PG+G+ G S + ++ + + + A A+G+F + E + + +EY Sbjct: 353 DPKPCVALVPGLGLFGIGASAKDAAIAADIAVNTVESITDAEAIGRFEPVGEADLFDLEY 412 Query: 409 WPLELYKLTLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQKIA 468 W LE KL A E +R+V ++TGG GIG+A + FA EG V V D + + A K A Sbjct: 413 WSLEQAKLGKA-AEKPLARQVVVVTGGGSGIGAATAKAFAKEGAEVAVLDRDADAAAKAA 471 Query: 469 GEINDAYGKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATSSPFDETSLK 528 G+A+ + DVT V++AF+R A +GG+D+VV+NAG A E Sbjct: 472 KACG-----GKALGIACDVTDPASVRAAFDRVAERFGGVDVVVSNAGAAWQGAVGEVDDS 526 Query: 529 EWNLNMNVLGTGYFLVAREAFKQMKHQNRGGSMVFVGSKNSVYAGKNASAYSSVKALETH 588 + + G+ VA+ A + K Q GG+++F SK +V GKN Y KA Sbjct: 527 TLRASFELNFFGHQAVAQNAVRVFKAQGTGGALLFNASKQAVNPGKNFGPYGLPKAATLF 586 Query: 589 LARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRTAL 648 L + A + G+ GIR N+V D + G + + R++A G+ E+ Y L Sbjct: 587 LMKQYALDHGKDGIRSNAVNADRIRSG--LLTDDMIKSRSSARGLS----EQDYMGGNLL 640 Query: 649 LVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGG 682 + ED+A+A + A KA K T C +TVDGG Sbjct: 641 GREVTAEDVADAFVWLA--KASKVTACTVTVDGG 672 Lambda K H 0.317 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 967 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 689 Length of database: 679 Length adjustment: 39 Effective length of query: 650 Effective length of database: 640 Effective search space: 416000 Effective search space used: 416000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory